| caFromDf {CalciOMatic} | R Documentation |
The function caFromDf applies the ratiometric transformation to
the vectors of fluorescence (including background fluorescence)
contained in a data frame and returns the corresponding intracellular
calcium concentration. The structure of the data frame is defined in
the ratioExpSimul function.
caFromDf(df, numTransient = 1, Plot = FALSE)
df |
a data frame of class "fluo_rawdata" containing all
relevant information (fluorescence transients, background
fluorescence, calibration parameters and exposure times). The
structure of the input data frame is defined in the
ratioExpSimul |
numTransient |
an integer: The index of the transient to analyse
in the input data frame df |
Plot |
a logical value: Set to TRUE to plot the calcium
transient deduced from the ratiometric transformation |
The way [Ca^2+] is estimated by the ratiometric
transformation is described in the help of the
caFromRatio function.
A vector of intracellular calcium concentration ratiometric transformation.
Sebastien Joucla sebastien.joucla@parisdescartes.fr
ratioExpSimul, ratioExpPhysio,
caFromRatio
## (0) 'Experimental' parameters
## Parameters of the monoexponential calcium transient
tOn <- 1
Time <- seq(0,10,0.1)
Ca0 <- 0.10
dCa <- 0.25
tau <- 1.5
## Calibration parameters
R_min <- list(value=0.136, mean=0.136, se=0.00363, USE_se=TRUE)
R_max <- list(value=2.701, mean=2.701, se=0.151, USE_se=TRUE)
K_eff <- list(value=3.637, mean=3.637, se=0.729, USE_se=TRUE)
K_d <- list(value=0.583, mean=0.583, se=0.123, USE_se=TRUE)
## Experiment-specific parameters
nb_B <- 5
B_T <- 100.0
T_340 <- 0.015
T_380 <- 0.006
P <- 1000
P_B <- 1000
phi <- 1.25
S_B_340 <- 100/P/T_340
S_B_380 <- 100/P/T_380
## (1) Create a monoexponential calcium decay
Ca_Mono <- caMonoExp(t = Time, tOn = tOn,
Ca0 = Ca0, dCa = dCa, tau = tau)
## (2) Simulate the corresponding ratiometric experiment
df_Mono <- ratioExpSimul(nb_B = nb_B,
Ca = Ca_Mono,
R_min = R_min,
R_max = R_max,
K_eff = K_eff,
K_d = K_d,
B_T = B_T,
phi = phi,
S_B_340 = S_B_340,
S_B_380 = S_B_380,
T_340 = T_340,
T_380 = T_380,
P = P,
P_B = P_B,
ntransients = 1,
G = 1,
s_ro = 0)
## (3) Get the noisy calcium transient from the data frame
Ca_noisy <- caFromDf(df = df_Mono,
numTransient = 1,
Plot = FALSE)
## (4) Plot the simulated noisy calcium transient
## over the ideal calcium transient
## plot(attr(Ca_noisy,"Time"), Ca_noisy, type = "l", col = "blue")
## lines(Time, Ca_Mono, col="red", lwd = 2)
## abline(v = attr(Ca_noisy,"tOn"), lty = 2)